Mass Effect: Pendulum
by xI Blackfyre Ix
Summary: Jack Walker has never questioned an order. Sometimes that has even meant the deaths of those he cares about. But Jack isn't prepared for the famous Commander Shepard. A woman who will make him question loyalties he never knew existed, even if that means defying the powerful and secretive Pendulum Order.
1. Chapter 1

**A/N: Hi there! This is my first ever fanfic so feel free to review etc.**

**Disclaimer: I do not own the Mass Effect universe or any of its characters, with the exception of Jack Walker, he is my own creation.**

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Chapter 1

A hail of bullets thundered into the wall to Jack's right.

At the sound of the impact he tensed, ready for a stray bullet to ricochet into him at any moment.

Teeth clenched tight Jack fumbled his belt, desperately searching for a spare thermal clip to reload his rifle. Eventually he felt the tips of his fingers brush the familiar feel of a full clip and hastily thrust the fresh ammo into his assault rifle.

Jack crouched low, knowing that if even a small part of him was showing above the low wall behind which he was taking cover then the mech's automated targeting system would lock on to him and it would be game over. He wouldn't normally have to be so careful but he hadn't had enough time to grab his armour from the locker beside his bed after he'd realised that the base was under attack. All he'd managed to do was to grab his M-8 Avenger assault rifle and a few thermal clips. Now though Jack was almost completely out of ammo and he was still several sectors from the Hanger Bay where he was hoping there would be a way off this station.

Wiping a stray bead of sweat from his glistening brow Jack spotted an open doorway along the corridor to his left. _I've got to make a break for it_. Checking that his weapon was set to fully auto and shifting onto his feet like a sprinter, he bolted.

The gap he had to close was only about ten metres but that would be more than enough space for the mech to target him. Jack felt the adrenaline burning in his veins as he pushed his body as hard as it could be pushed. All the while he was spraying bullet in the mech's direction.

As he was about half way across he spotted the two mech's that had been keeping him pinned for the last quarter of an hour. Keeping his finger hard down on the trigger Jack felt a slight relief when he spotted one of the mech's take a bullet through its mechanical head.

_Four metres to go_.

The moment of glee didn't last as no sooner had he dropped the first mech than the second had raised his weapon, a signal that it had acquired its target.

_Three metres, nearly there_!

Jack's assault rifle made the horrifyingly familiar clicking sound signalling that it was out of ammo. Knowing that he needed as much of an advantage as possible he threw the weapon to the side and continued the dash.

_One metre_!

The mech fired.

Knowing that the shot was moments away Jack dived for the safety of the wall. The round clipped his left arm as he came careering through the automatic doors.

Despite the searing pain and the smell of burnt flesh from his arm Jack wasted no time getting to the keypad by the side of the doors and locking the door through which he had just come bursting through. The sound of two rounds hitting the sealed doors hung momentarily in the air, a reminder that he needed to keep moving if he wanted to get off the station alive. The pain in his arm flared and Jack decided to check that damage. He pulled the 9in combat knife that he kept tucked in his right boot and cut away the cloth around the wound. After that he scanned the wound using his Omni-tool to check for any infection or damage to the muscle or bone even though he knew he couldn't properly treat it as the medi-gel at the station was securely stored so as to curb any potential addiction to it. Luckily for Jack the bullet seemed to be little more than a flesh wound, also the wound had been cauterised which indicated to Jack that the mech's had been using incendiary ammo, something that – providing he escaped – bought him more time to treat the wound later on.


	2. Chapter 2

**A/N: It occurred to me that the previous chapter was a lot shorter than I had thought it would be. So from now on I'm going to make them longer :)**

**Disclaimer: I do not own the Mass Effect universe or any of its characters, with the exception of Jack Walker, he is my creation.**

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Chapter 2

The sounds of a firefight echoed around the station as Jack proceeded cautiously down a corridor. The lights to the corridor had been knocked out during the initial phases of the attack on the station meaning that the dim emergency lighting had kicked in. Jack slid quietly along the wall of the corridor using its cool, hard surface as a guide. Armed with only his combat knife and being hampered by the gunshot wound to his left arm Jack was aware that his chances of reaching an escape shuttle, if there were any left at all, were now exceedingly slim. It was exceptionally rare that a Cerberus base was caught off-guard like they had been, even rarer with one as heavily guarded as the one Jack was on._ But therein lies the problem_ Jack mused. The reason that the men and women stationed there were being so heavily beaten was because the majority of the security relied heavily upon the stations army of mechs. So when they began attacking everything in sight, combined with the fact that most of the personnel were scientists, there were very few people with the ability to fight back.

The gunfire that had at first been ever-present whilst Jack was moving was now becoming very sporadic. _There can't be that many of us left. Shit. I'd better not be too late – _Jack stopped. A noise on the other side of the doors at the end of the corridor caught his attention. He glided to the frame of the doors, ready to pounce on anything that came through them. He slowed his breathing to reduce sound and to increase his hearing. There was movement. Crouching low and raising the steel knife to a striking position Jack waited. For what seemed like hours but was probably less than five minutes Jack remained perfectly still, a technique he had grown used to over his years of covert operations, first for the Alliance and then also for Cerberus. Suddenly, breaking the silent deadlock Jack heard the input of a code on the other side of the doors. After a few painstaking seconds a figure moved through the doorway. Like a tiger taking out its prey Jack jumped up immediately smashing a clenched fist onto the emergency shut doors sign so as to stop any more of them following. Then in an effortless motion he swung into a roundhouse, smashing the pistol out of the startled figures hands. Quickly regaining his footing Jack smashed his well-muscled and broad shoulders into the opponent, sending them sailing into the wall on the opposite side of the door. Jack heard the unmistakable sound of a bone breaking. Waiting for the sudden onset of pain he was surprised when none came and was replaced with a dull moan from the crumpled figure on the floor.

"Miranda!" He exclaimed, eyes widening in surprise. Immediately before the radio had cut out there was chatter that Miranda Lawson had been killed over in D-wing at the start of the attack. Jack was relieved to find out that it wasn't the case.

"It's good to see you alive Jack." Miranda replied in a pained, husky voice as she slowly raised herself off the ground.

Suddenly remembering the protocol that had been drilled into him during his time in the Alliance military, Jack helped his superior up before switching to a salute.

"Sorry about the surprise ma'am." He said when he noticed her wince whilst retrieving her weapon.

"Yeah, I tried to tell you but you knocked the wind out of me." she said tentatively rubbing her torso and waving away his attempt at more apologies, "I think you broke a rib too."

"Are you heading to the shuttle bay?" Jack asked as Miranda handed him her spare pistol.

"Yes. Hopefully Shepard will meet us there."

"You woke her up?" He asked in surprise. From all the reports over the last few weeks Jack knew that, at best, it would be about two or three months before they would attempt another awakening..

"Well I didn't exactly have much choice."

"The Illusive Man isn't going to be happy." Jack noted. When Miranda turned to glare at him he knew he'd said the wrong thing.

"He's going to be a lot happier with her alive and scarred as opposed to dead! Which unless you've forgotten the last two years, wouldn't be any progress."

"Understood ma'am." Was all Jack said in reply, something that made Miranda slightly more annoyed. She thrived in stressful, challenging situations and hated it when people didn't put up a fight. Miranda shifted her gaze to the wound on Jack's arm. Bringing up a her omni-tool Miranda applied a dose of medi-gel to his arm. She wished she could fix her rib the same way but unfortunately the injury was under the skin and would have to heal the old-fashioned way, with time and a healthy supply of aspirin. She was disappointed in herself for letting Lieutenant Walker ambush her, it was very rare that she came off second best in a fight, her genetic modification all but guaranteed that, she promised to never let it happen again.

"If we want to make it to the shuttle then we'd better get going." Miranda ordered bluntly. Jack reloaded his pistol and fell in behind the Chief Operative.

They spent the next twenty minutes quickly but professionally going from room to room, sector to sector until they had made it to the shuttle bay. Along the way Jack had hoped to pick up and survivors but the closer they got to the hanger he became less optimistic. Despite his vain hope Jack also knew it was no coincidence that he, Operative Lawson and possibly Commander Shepard were the only people left. Miranda Lawson was one of the biggest assets that Cerberus possessed, not just as a soldier but also as a scientist. It was no accident that the Illusive Man named her as head of Project Lazarus, the project to resurrect Shepard from the dead. Likewise, with the exception of Miranda Jack was one of Cerberus' best soldiers. Five years in an Alliance Black Ops team and three years for Cerberus had turned Jack into a weapon, one which the Illusive Man had no problem with using.

"Ok, are you ready?" Miranda checked, looking over her shoulder to Jack. Jack nodded his assent, something he had done a thousand times before today. Miranda punched in the code to the hanger bay where she hoped there might still be a shuttle. The door opened and like a well-oiled machine Jack and Miranda entered, weapons raised ready to clear any opposition in the room.

"Clear." Miranda sounded.

"Clear." Jack echoed as they holstered their weapons.

Jack struggled to contain his relief at the sight before them. His gaze rested on a workable shuttle. It was an older model than what was normally being used by Cerberus and indeed the Alliance but after Miranda had a look around the cockpit and gave a thumbs up Jack couldn't care less. There had been points over the day where for a few moments he had honestly believed that he wasn't going to survive. Whilst Jack sat down in the pilots seat and began to get the shuttle ready for flight Miranda moved to the door on the other side of the hanger._ Probably keeping a look out for mechs_. No sooner had the thought occurred to him than they heard the sound of the door opening. Jack moved to the shuttle exit, crouched, ready to fire at the first sign of trouble. Miranda however stood unmoving at the entrance.

From his vantage in the shuttle things were unclear. Jack felt a moment of relief when the doors opened and he saw a Cerberus uniform filled by Dr Wilson, the Chief Medical Officer. But his happiness was short lived when Miranda calmly raised her weapon and shot him through the neck, a clean kill. Jack had never liked Wilson but seeing him executed in that way was disturbing. It had been a long time since Jack had witnessed such cold-blooded, merciless killing. Only back then he hadn't exactly been the bystander as he remembered with a touch of guilt. Despite his shock at the killing Jack knew better than to question the actions of Miranda. If she'd done something like that then there were reasons.

Beads of sweat trickled from his thick dark brown hair as Jack watched as two more figures appeared in front of Miranda. He kept his finger firmly on the trigger of his weapon, ready to fire if he felt the need. When Jack recognised one of the figures as a tired and very confused Jacob Taylor he released the tension on the trigger. Jacob may not be one hundred percent behind Cerberus all the time but he'd never attack Miranda. Jack had crossed paths with him whilst they were both in the Alliance so when they met again at Cerberus they quickly became good friends thanks to their common history and employment.

Jack was lost for a moment when he saw the person in Jacobs company. He's spent so long seeing her on an operating table that to see her on her feet and conscious was a shock. Commander Ellen Shepard had her weapon pointed at Miranda, threatening but in no way malicious. She was slightly taller than the Chief Operative making Jack guess that she was about five foot nine maybe ten meaning that she was about four or five inches shorter than himself. She had shoulder length dark red hair and a light complexion that seemed to glow in the artificial light. He couldn't deny that she was striking, something that wasn't apparent until now. After exchanging a few words with Miranda she lowered her weapon, seemingly satisfied with whatever Miranda had told her, moments later they started towards the shuttle.

"Commander, this is Lieutenant Walker." Miranda said introducing Jack as they boarded the shuttle.

"Good to meet you Lieutenant though I'm guessing you probably met me a while ago now." Said Shepard, indicating her two year tenure at the Lazarus Research Station. Jack formed a crisp salute.

"Yes ma'am but it's good to properly meet you."

"You can just call me Shepard." She suggested, hating the formality of ma'am or sir.

"Will do." Jack turned his attention to the man now stepping up towards him. "It's good to see you alive man." Jack said grabbing Jacobs hand and giving it a heavy shake.

"Yeah you too Jack, I thought you were a gonna for sure." Jacob said with a broad grin on his chiselled and roguish face.

"Ye of little faith." Jack turned back to Miranda as she closed the doors. "Where are we headed?" Jack asked, not even bothering to mention the death of Dr Wilson knowing that he'd get an explanation on the way.

Miranda slumped into the seat next to Jacob and opposite the Commander. Despite being visibly exhausted she couldn't help but smile.

"I think Shepard has an overdue appointment with the Illusive Man."

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**Feel free to review etc. I'm always open to suggestions.**

**I'm going to try to keep updating this on a regular basis so if it is a little while before chapters are published then don't worry it means it'll be a good one!**


	3. Chapter 3

**A/N: I've decided that because it's easiest for me I'm going to upload one chapter a week on a Monday. If something changes and I happen to upload more than one chapter in a week then consider it your good fortune! I hope. Also I welcome feedback on my stuff so feel free to review etc.**

**Disclaimer: I do not own the Mass Effect universe or any of its characters, with the exception of Jack Walker, he is my creation.**

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Chapter 3

"We should be at Freedoms Progress shortly Shepard, The Illusive Man put us under your command. Do you have any orders?" asked Miranda in her best 'business as usual' tone.

"Are you sure you'll be comfortable following my orders? Shepard asked, eyebrows raised. Jacob decided to speak up for his superior knowing that she wasn't the type to sugar-coat things.

"We didn't bring you back from the dead just to second guess you commander. If the Illusive Man says you're in charge, then you're in charge." Jacob said making the palpable issue of Shepard's authority absolutely clear. Shepard took a moment to look around the group before speaking.

"Our first priority is to look for survivors."

"That's unlikely commander, no one was left at the other colonies, they were completely deserted." Miranda pointed out, the first of many subtle rebellions against her new commander. She was not used to being second in charge and the fact that the Illusive Man had put her in charge despite being dead less than forty-eight hours ago was, in her mind, a serious risk considering the volatility of the mission. She believed that the escape from the research station was an insufficient test of her recovery, particularly since she didn't see most of it for herself.

"It'd be nice to find somebody." Jacob chirped in. "Anything is better than another ghost town."

"Thirty seconds until we land." Jack called from inside the shuttles cockpit. Spotting a decent spot to land he dropped altitude and switched on the thrusters in order to cushion the landing. Once he'd set the shuttle down and turned off the controls Jack went through to the seating area of the shuttle. He spotted Commander Shepard grabbing an assault rifle from a locker.

"Commander." Shepard turned to face him.

"Lieutenant Walker, right?" she asked.

"Yes Commander."

"Is there something I can do for you?" she asked crossing her arms, an indication that she still didn't trust Jack or anyone on this mission.

"I'm requesting permission to remain with the shuttle." Jack asked, standing to attention, his face impassive.

"On what grounds?"

"On the grounds that we don't know who the attackers are or whether they're still here. By staying here I can protect the shuttle and be on standby in the event that an extraction is needed."

Shepard looked sceptical and turned towards Operative Lawson for advice. Shepard was still uncomfortable around her new second in command, especially after how she'd dealt with Dr Wilson back on the Lazarus Station but she was aware that Miranda was a better judge of the Lieutenant. A slight nod from her was all it took for Shepard to agree. Jack suspected that Miranda was also curious to the reason why he was electing to remain with the ship, knowing first hand that he was more than reliable in a fight but she decided not to say anything, probably another subtle rebellion.

Jack waited patiently for them to ready their gear and leave before he finally meandered over to his locker. From there he selected a radio headset that fitted neatly into his left ear.

"Cerberus High Command this is Echo three, over."

"Echo three this is HQ, how can I be of assistance, over."

It had been at least six months since Jack had done this but he still remembered the protocol. Certain quotes from the bible represented whom you needed to be patched through to. Jack suspected that the Cerberus operator hadn't often heard this one.

"To every thing there is a season, and a time to every purpose under the heaven."

"Patching you through, Echo three."

Jack wondered whether all the code was necessary, he was aware that the order had many men within Cerberus, enough that it was essentially at their disposal. Yet the Illusive Man had been very clear on his instructions after they had arrived from the research station. The protocol must be observed.

"Lieutenant Walker, I have your mission details here, are you ready?" the voice asked. Jack could tell from the accent that the person was human but the voice scrambler being used made it difficult to be more specific.

"Yes Sir."

"Just to be clear this is straight from The Chairman himself, no room for error."

"Understood Sir." Jack assured the mysterious voice.

"Recently a Quarian named Veetor managed to hack in to the Orders archives. He wasn't able to copy any data but he may have memorised some of the files relating to the identity of several well-positioned Pendulum servants."

"So you want me to take him out?" Jack asked coldly.

"No. On the planet right now is a team of Quarians being led by Tali'Zorah nar Rayya. Among that group is a member of the order, his name is Prazza." Jack recognised the name Tali as a member of Shepard's previous crew but had never heard of Prazza. The voice continued. "Prazza will attempt to get the names from Veetor and expose them. You cannot let that happen. We want you to make sure he never gets to Veetor."

"How will I find him?"

"The colony is small. Tail Shepard's group. They'll run in to the Quarians eventually."

"What made Prazza betray us?" Jack asked out of curiosity. There was a slight pause before the reply.

"That's not relevant to your mission Lieutenant." The man said slowly, making it clear to Jack that he shouldn't probe any further.

"In which case sir I understand my mission. Prazza will not reach Veetor." Without another word the channel closed. Jack sighed. He hated being used as a hitman, it made him feel like he was nothing more than a means to an end. Indeed he regretted his involvement with the order. Ever since he had been initiated by his father shortly after he joined Cerberus he had come to realise that Pendulum was very dangerous, the irony of his thought didn't escape him as Jack knew he was a big part of why that was.

Switching the channel on his headset to the same one that Shepards team would be using Jack reached into his locker. Knowing that he was quite far behind Shepard and the group he decided against heavy armour and decided to just use simple combat fatigues so that he could travel light and quick. He pulled an M-92 Mantis sniper rifle from the locker as well as having an M-6 Carnifex heavy pistol strapped to his right leg. After fixing a silencer to the rifle and checking his ammo pouches, Jack set off.

It took him quite some time to locate Shepard. He had to go through endless amounts of buildings before he saw them through the window of another building. Jack crouched behind the wall and rested his rifle on the windowsill, looking over towards Shepards group. She was talking to someone. _Please be the Quarians,_ Jack hoped. He wanted nothing more than to be done with this mission, then maybe the order would leave him be for at least another few months. From his vantage point Jack shifted a few feet to his left so as to get a clear view on who Shepard was talking to. It was a Quarian. _Thank God_, he thought to himself. Jack checked the windage and the range to the target. Then he slowed his breathing to steady the rifle. Satisfied that he would hit the target Jack rested his finger on the trigger of the rifle, the fluidity and familiarity in which he performed the ritual was almost soothing to him. He began to lightly squeeze the trigger, ready for the rifle to recoil as the round exited the weapon and did what hundreds before it had done. He was just about to reach the point of no return when he stopped. Releasing the trigger Jack swore under his breath. Another Quarian had appeared in the scope. He realised he had no way to tell the difference between them. Then it hit him. Jack loaded up his omni-tool and programmed it to listen to the conversation that was going on three hundred metres in front of him. From the chatter it became apparent to him that the figure he had been aiming at was Tali'Zorah and that the other figure was Prazza. _Sounds like a bastard_. Jack readjusted his rifle, repeating the previous motions until the scope rested on the target's head. He was just about to complete his mission when Jack heard a noise from behind him.

"Hostiles." In the doorway of the building Jack was occupying a mech come in to view. Jack spun, reaching for his pistol but he wasn't quick enough. The mech fired hitting Jack in the thigh. Scrambling for cover Jack knocked over a nearby table for cover. The pain was excruciating making him wish he'd brought the armour after all. Unlike on the research station this mech wasn't using incendiary rounds and blood was starting to ooze from the wound. Another round hit the table to his left, punching a hole clean through. Jack spotted the pistol over by the wall, he guessed he must have dropped it whilst he was moving position.

Jack counted to three.

Then he rolled.

Scooping the weapon off the ground Jack moved like lightening firing three rounds in quick succession. The first round hit the frame of the doorway behind the mech but the following two punched clean through the mech's chest, destroying it. Suddenly his headset clicked, a signal that someone had opened the channel up and was about to speak.

"Shepard!" It was the Quarian leader, Tali. "Prazza and his squad rushed on ahead, I told them to wait but they wouldn't listen! They want to find Veetor and take him away before you get here!"

"We should have expected this." Miranda said, annoyed.

"We can still catch them!" Jacob insisted.

"Lieutenant Walker." Jack recognised the voice as Shepards. Jack fumbled for the switch that allowed him to speak, smearing blood on the headset in the process.

"Yes Commander." Jack responded feeling slightly light-headed.

"We're going to need the shuttle to catch up with the Quarians. Pick us up."

Jack panicked. He was just as far away from the shuttle as they were and he was losing a lot of blood, he had to think of something.

"There was a mech attack and the shuttle's taken some damage, I'm going to need time to repair it." Jack hoped the deception worked.

"Are you hurt?" she asked. Knowing that he would have to explain the wound eventually he decided to limit the lie.

"I've been hit and I'm losing blood but it's not too bad." Jack ground his teeth together as a spike of pain shot through his leg.

"Do you require backup?"

"Negative Commander." Jack held his breath. If Shepard sent someone back then there was a good chance that he wouldn't make it to the shuttle before the backup did, it also meant that he'd never get to Prazza. The silence continued as Shepard debated with herself.

"Copy that Lieutenant. Keep working on those repairs." The headset clicked, ending the conversation. Jack let out a sigh of relief. He then pulled up his Omni-tool and applied some medi-gel to his thigh. It would require attention when he returned to the Normandy but as a temporary solution it would serve. Then, gathering his rifle, Jack set off after Prazza.

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Up ahead Commander Shepard could hear the tell-tale signs of battle. She took cover behind a large, white container as Tali opened up the doors to the Loading Bay. She had been concerned when the Lieutenant mentioned he'd been shot. She could tell from his heavy breaths that the wound was worse than he was letting on but she didn't want to insult him by sending someone back, plus she was confident that she needed both Jacob and Miranda with her in the event of any more mechs. As soon as the doors to the Loading Bay opened Shepard moved immediately for the nearest cover behind a supply crate that at one time was destined for The Citadel. The Bay was a warzone. A YMIR heavy mech was guarding a building on the opposite side of the compound. In between the mech and Shepard were half a dozen dead Quarians. Shepard guessed that in his rush to reach Veetor, Prazza had stumbled straight into the heavy mech and they were being torn apart.

"Commander Shepard!" One of the Quarians came scrambling up beside her to take cover from the slaughter in front. She turned to face the alien, recognising him as Prazza, the one who had been so eager to steal Veetor from under Shepards nose. "Commander I made a mistake not trusting you." He conceded. "When I saw that you were with Cerberus I assumed that you might be one of them." Shepard was confused but decided to play along with his ramblings.

"What convinced you I wasn't '_One of them'_?" She asked, curiosity peaked.

"You would have shot me dead as soon as you heard my name." The Quarian stated.

"Why would I do that?"

"Because of what I'm looking for. Because of what I intend to do."

"And what exactly is that?" she probed.

"I –" Shepard ducked. As Prazza was about to talk a bullet sliced through the Quarians neck, splattering Shepard with blood. She looked up towards a balcony where the shot must have come from but saw nothing. On the floor the Quarian was convulsing violently. From the gurgling sounds she knew he was dying, chocking on his own blood. Suddenly his hand grabbed her arm in a vice like grip, pulling her down towards him. He was trying to say something but the blood stopping him. Then, she recognised that he was choking out a single word over and over again. Pendulum.

"What's Pendulum?" She shouted over the gunfire as Jacob and Miranda finished taking down the heavy mech. She felt the grip on her arm loosen as the life left Prazza, then as if he'd simply gone to sleep, the gurgling stopped. He lay there. Unmoving. Completely still. His final words were all Shepard could think about as she entered the building where Veetor was hiding. Completely unaware of the significance of the information he possessed.

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**I'm proud that I already have four followers and two favourites for this story. I'm not really sure how good that it but it makes me happy none the less. To those of you who have followed and favourited (you know who you are!) you have my thanks for supporting this story early on. :)**


	4. Chapter 4

**A/N: Well here's chapter 4 as promised! I hope you enjoy it. As always feel free to review etc. it's always accepted.**

**Disclaimer: I do not own the Mass Effect universe or any of its character, with the exception of Jack Walker, he is my own creation.**

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Chapter 4

"You're a very lucky man lieutenant." Dr Chakwas explained as she opened the top draw of the medicine cabinet by the side of the bed that Jack was lying on. Jack replied without even opening his eyes. A stray arm draped across his forehead.

"Sometimes I find that hard to believe." He said dryly. Next to him the doctor opened the top draw of a portable medicine cabinet and pulled out an empty syringe.

"The medical facilities here on the Normandy are far better than those on the station. Also I hear that the standard of care is much better here." She said with a smirk. Jack smiled. The unveiling of the Normandy SR2 was as much of a surprise to him as it was to almost everyone else. _Except for Shepard, of course_. According to Jacob her excitement at the sight of the new vessel was nothing short of palpable, although according to him she was still too distrusting of Cerberus to let it completely show. Jack understood. He knew that Cerberus didn't do anything for anyone unless there was a greater purpose in mind, something he had learnt as soon as he'd been recruited. Jack sat up on the bed and dangled his long legs over the side.

"What's the needle for?" He asked cautiously. Jack hated needles. He could deal with being shot at, blown up or even angry clowns but for reasons he couldn't fathom, he couldn't stand a tiny injection.

"The syringe is filled with a chemical that, after I have injected into you, will allow me to assess the damage to your leg once you have been x-rayed." She explained casually. Jack gulped. Dr Chakwas' head turned towards the door.

"Ah, hello there Commander." She said, greeting her old friend. Jack was aware of the doctor's service on the previous Normandy. Jack turned towards the Commander. He couldn't help but notice how the Cerberus uniform fitted her much better than armour.

"Hey Doc." Shepard replied familiarly. She looked at Jack, her deep green eyes radiating in the glow of the artificial light. "Lieutenant." She said with a nod, her dark red hair rested lazily on her shoulders.

"Commander." Jack replied with a salute that was made somewhat difficult by his position.

"Is there something I can do for you, Commander?" The doctor asked Shepard, uncomfortable with the breach of doctor-patient confidentiality.

"I was just touring the ship, getting to know the crew." She offered by way of explanation. "I was told that the lieutenant was here. Doctor Chakwas stuck the needle into Jack's arm, taking him off-guard.

"Ouch! Why not in the leg?" He suggested, knowing that the medi-gel would have a numbing effect. The Doctor pushed him back down and switched on the x-ray machine. It hummed loudly for a few moments before she had finished. Jack sat back up.

"I'd like to get a copy of your whole skeleton to put on record, they'll just take a few minutes to develop." She turned her attention back to Shepard. "He's all yours Commander." She said, disappearing to the other side of the room.

"Thanks Doc." Shepard said, smiling as Jack rubbed his arm. She took a seat on the bed next to him. "How bad is your wound?" she asked, indicating his leg.

"We'll know soon enough." Jack replied with a nod towards the doctor. He paused for a moment. "Did you get anything from Veetor's omni-tool?" he asked pensively.

"Nothing we didn't already know." She looked down to her knees, her brows furrowing in annoyance. She was obviously used to getting results. Jack guessed that she missed her old team. She raised her head to look back at the lieutenant. "Do you mind if I ask you a few personal questions? I want to get a feel for my new crewmates."

"Ah, yeah, sure thing." He answered. "What do you want to know."

"Well," she paused, thinking of what to ask. "Where were you born?"

"Shouldn't that be in my file?"

"I don't bother with files. In my experience they rarely tell you anything about a person." She answered honestly. Jack could easily appreciate the logic behind her reasoning. He knew that files could easily be doctored or well-worded in order to cast a better light on somebody who probably didn't deserve it.

"Well, I was born on Earth in a town called Raleigh, which is in North Carolina in the United States. I lived there until I was about four when my mother died and so I moved to Georgia to live with my mother's parents."

"I'm sorry about your mother." Shepard said sincerely. "What about your dad?" Jack looked away.

"He wasn't around." He said evasively. Shepard took the hint.

"My mother wasn't around much for me either." She explained, knowing his pain. She decided to capitalise on the common ground they shared. "Mr Taylor tells me that you served in the Alliance."

"Yeah I enlisted when I was eighteen, spent three years as a normal trooper before I was drafted into an Alliance Black ops unit where I served as a marksman. I did that for another five years." Shepard looked impressed.

"Those are quite the credentials. Why did you leave?" She enquired.

"I was honourably discharged." He said with a snort of derision. Jack hoped that she would leave it there.

"Go on." She pressed. He sighed.

"One day my unit got a call that a human colony called Akuze had gone quiet. The Commander of my unit, Captain Anna Herd, ordered the entire unit there to investigate the situation." A bead of sweat ran down Jack's temple. "She explained to us that it would be bad for the Alliance's chances of securing a council seat if one of our colonies's was attacked or destroyed. She sent our entire unit, fifty one men in total." Shepard sat quietly as he continued. "When we got there the place was deserted. Not a soul in sight. The leader of the team ordered us to make camp for the night amongst the abandoned buildings, he decided that we would mount a better search in the morning." By now Jack's voice was starting to shake, Shepard reached over and put her hand on his. It was gentle, a sign of comfort, a signal that he wasn't alone.

"Keep going." She encouraged, not removing her hand. Jack swallowed hard.

"My sniping partner and me snuck away in the night to have a look around. It was in our nature to know the terrain as well as possible, we might have needed to set up at some point." Jack hesitated. The warm feel of Shepard's soft skin on his own reassured him, he continued. "When we came back to the camp it was…they…were everywhere. Thresher Maws. There were dozens of them. My partner and I tried to help the fight but it was relentless, they didn't stop. I got knocked out during the fighting and when I came to…" Jack's voice caught in his throat. He felt like he couldn't breathe, it was almost as if he were there once again, wandering aimlessly amongst the corpses of his fallen comrades. Shepard knew what happened after that, it didn't take a genius to guess.

"Why did they discharge you?" She asked after a few minutes, giving the lieutenant time to recover. Jack took a deep breath.

"I knew that the Alliance would just sweep it all under the rug and I couldn't let that happen. Fifty good men died for nothing!" Jack shouted, drawing an annoyed glance from Dr Chakwas who was going over Jack's X-ray's. He continued. "So instead of reporting back to the Alliance, I went straight to a journalist." Shepard understood. Jack had broken Alliance protocol by giving details of a sensitive mission to the press. Under normal circumstances he would have been court-martialled. However because of the nature of the mission and the fact that he'd won the protection of the newspapers they couldn't submit him to punishment, which was the only reason why the discharge wasn't a dishonourable one instead of an honourable one.

"I understand." Was all that Shepard said. Jack smiled. She hadn't needed to say anything more. He could see it in her eyes. It was the look of someone who had gone through a nightmare. Jack saw the same look every day in the mirror. He wondered to himself what had been so terrible that made her able to sympathise with him.

Suddenly they were both aware that her hand was still on his.

She withdrew it quickly, looking away.

Dr Chakwas came over, sparing her Jacks look of confusion. He wasn't sure why see had pulled it back so quickly._ Is she embarrassed about something_?

"I reiterate my point Lieutenant." Dr Chakwas said holding Jacks X-ray to the light. He tore his gaze from Shepard and turned towards the doctor. "You are indeed a very lucky man. Eight millimetres to the left and your femoral artery would have been severed. Had you then applied the medi-gel you would have sealed both ends of the artery and you would have lost most of the blood circulation to your leg."

"What would that mean?" Jack asked baffled.

"Amputation." The doctor replied bluntly.

Jack let out a low whistle. Even Shepard looked slightly concerned.

"As it is you should make a full recovery within about two days without any need for surgery. I recommend that you get some rest. It will aid the healing."

Shepard turned to him.

"Sounds like you got lucky." She said, refusing to meet his light blue eyes.

"So I'm constantly reminded." Jack joked. They both knew that she didn't just mean the injury.

Shepard jumped off the bed, breaking the silent tension that had engulfed the medical bay.

"Well I had better get back to touring the ship." Shepard announced heading towards the door. She stopped, looking back over her shoulder. "I look forward to working with you Lieutenant Walker."

"As do I, Shepard." He muttered under his breath as he watched her leave. "As do I."

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**I hope that you enjoyed this chapter as I understand that it's very different from my previous ones. It was actually a lot tougher to write this chapter than I thought it would be but I like to think it turned out okay in the end.**

**Until next week...**


	5. Chapter 5

**A/N: Hi there! Just thought I'd say thanks to my followers, it means a lot to me to know that people actually want to read this stuff. Also a thanks to everyone who's taken the time to drop a review, I'm always open to your thoughts etc.**

**Disclaimer: I do not own the Mass Effect universe or any of its characters, with the exception of Jack Walker, he is my creation.**

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Chapter 5

_A dry, swirling wind whistled through the winding, sullen valley. Amongst the lance shaped Cyprus trees that adorned its sloping walls, Jack Walker waited patiently. He allowed beads of warm, grimy sweat to trickle aimlessly down his dirt-encrusted face, not bothering to wipe them away despite the almost unbearable irritation. _

_He remained perfectly still. A vigil amongst the sands._

_The sharp, jagged edge of a rock was attempting to puncture its way between his bottom two ribs. The pain served to keep him focused and awake. _

_He checked the watch that was set up next to the barrel of his rifle._

_ Three minutes. _

_In the distance he could see heat waves vibrating on the rough, bare road that snaked along the valley floor. Slowly, he shifted the heavy rifle so that it rested neatly into the nook of his shoulder, his left hand placed underneath the butt so as to steady the rifle. Looking through its scope, the vast expanse of desert beyond the entrance to the valley became visible to him. On the crest of the horizon, Jack could see the shroud of dust that was encasing the target vehicle. Carefully, Jack reached for the microphone on his shoulder._

"_Target sighted. ETA to kill zone, one minute. Over." On the other end, Jack heard the mic crackle._

"_Roger that, Kilo Six. Proceed as planned. Over" The mic switched off. Jack continued to follow the approaching vehicle through his scope before he shifted his right hand so that his index finger rested gently on the trigger. Inside the vehicle were two men, the driver was a Batarian and the passenger was a Turian. _

"_An unlikely combination." Jack whispered to himself. Jack's orders were to take out the Turian, and if he became a problem, then the Batarian was expendable too. By now the face of the passenger was clear, Jack could see that he was reading something on his datapad._

_Then, without hesitation or remorse, he fired._

Jack shot up. His breathing was ragged and heavy and the bed was soaked with his sweat. His hand darted for the glass of water on his night stand and quickly gulped the whole thing down. Jack sighed. This wasn't the first time one of his past exploits had haunted his dreams. What worried him the most is that they were becoming more and more common. Every single time he would wake up covered in sweat and breathing as if there was no oxygen in the room. Sometimes he debated acquiring some medication from Doctor Chakwas, but he was aware that any drugs could potentially diminish his performances in the field, thereby putting himself, and his squad mates at risk. Switching his gaze to the clock next to his bed he saw that it read six o'clock. _I could do with something to eat_, he reasoned. Pulling on a plain black t-shirt and his Cerberus issue combat trousers and black boots, Jack made his way to the mess hall.

Once Jack arrived at the hall he saw that there was nobody around except for Mess Sergeant Gardner, who by the looks of things was just finishing the preparations for the days breakfast. Jack grabbed a tray and wandered over towards the cook. Gardner must have heard someone moving because he tore his concentration from cutting fresh fruit and turned to face Jack.

"You look like shit." Was his greeting. Jack uttered a dry, thoughtless laugh. It was still early enough that he appreciated the cook's gruff honesty and sense of humour.

"Thanks Rupert." Jack replied, "What's on the menu this morning then?" Gardner grunted, obviously unhappy.

"All I've got is this damn fruit and porridge." He moaned, indicating towards the meagre meal in front of him. "If it was up to me I'd get in some quality ingredients and you boys could have proper meals, not this military crap!"

"Maybe you should talk to the Commander about it?" Jack suggested with a smile. It amused him how a man like Gardner could be so passionate about what goes into another man's belly. The Sergeants eyes lit up as he considered Jacks plan.

"That's a great idea!" He bellowed in his characteristic voice. "But in the meantime how about some of this porridge?" He said with a wink as he scooped the metal ladle into the sludge-like substance. Jack felt his stomach turn.

"I think I'll pass on the porridge, thanks." Jack said as some bile attempted to fight its way up. "But I will have some fruit though, and a glass of water." The Mess Sergeant shrugged.

"Suit yourself." He said, loading Jacks tray with an assortment of food. Jack thanked him and sat down at the table nearest the counter. He started wondering why the nightmares were becoming more frequent. _Perhaps it's my conscience catching up with me_, he pondered wryly.

He jumped at the sound of a tray thumping down in front of him, quickly pulling him from his thoughts. Jack looked up.

"Oh, good morning Commander." He said as Shepard sat down across from him. Aside from the two of them and Gardner, the hall was still empty.

"You looked like you were deep in thought." She said toying with her porridge.

"Yeah, I guess I was." Jack replied absently. Shepard frowned, picking up on his tone.

"Anything you want to talk about?" Jack peered up from his food, looking into her face. He could see that her question was serious, if somewhat intrusive.

"Just a bad night's sleep." He said, returning his attention to a sweet looking red apple. "That's all."

"It's rarely as simple as that."

"Speaking from experience Commander?" He said. There was a brief, yet noticeable silence before the reply.

"Something like that." Jack looked back up, realising his insensitivity. It was then that he finally took in her appearance. Her hair, normally so immaculate, was slightly dishevelled. Her eyes drooped with exhaustion. Despite her haggard look, she was still striking. Jack was still getting used to having a commander only two years his senior. At thirty-one she was being asked to bear the responsibility of someone who should be much older – it was easy to forget that.

"I'm sorry Shepard." He said, "Being a sniper most of my career makes it tough for me to stop taking shots at people, whatever the form. It wont happen again." He promised. Shepard smiled at him as she chewed on her food.

"Don't worry about it Lieutenant. I wouldn't be much of a leader if I couldn't take a bit of the truth once in a while." She said, laughing. Jack smiled. Suddenly he was beginning to feel his mood lift.

"Look Shepard, I know that you don't trust Cerberus, and to be honest that's probably a good thing, The Illusive Man has a habit of keeping people 'out of the loop' - "

"What's your point, Jack?" She interrupted gently, her soft gaze resting on his face. He smiled at the use of his name.

"I just want to say that even if you don't trust Cerberus, you can at least trust me." Shepard was visibly touched by his statement.

"Thank you Lieutenant," she said reverting back to rank, "that means a lot to me. Mr Taylor said something similar before we left for Freedom's Progress."

"Jacob's a good man, you can rely on him."

They were spared any awkward silence by the arrival of a group of marines who were talking to each other very loudly. _I hate morning people_, he thought to himself. Shepard laughed. Jack realised that he'd accidently said it aloud as the annoyed marines glared at him.

"I know the feeling." Shepard whispered conspiringly. Before he had time to laugh they were joined by Joker, who sat next to Shepard, something that Jack took to be a sign of his loyalty to her as opposed to Cerberus. Jack disliked being its personification.

"We'll be arriving at Omega in about three hours Commander." Joker said, ignoring the Lieutenant.

"That's good Joker, thanks."

"So I guess you'll be going after the good doctor? That ought to be a blast."

"We need him to create a counter-measure for the Collector swarms." Jack chimed in.

"Yeah, I know." Joker said confrontationally. Jack sometimes found it hard to believe that the Normandy's helmsman was still a Cerberus employee. When the lieutenant didn't respond, Joker turned back to Shepard.

"Who will you be taking with you Commander? I'm gonna need to know who I'll be babysitting." Joker asked with a side glance at Jack who merely rolled his eyes and continued to disembowel a particularly tasty kiwi.

"I think I'm going to leave Miranda behind. She can be a bit testy and the last thing we need is to start a fight - especially on Omega. Besides," she continued, "the Lieutenant here will have my back, won't you Jack?"

"As if it were my own." He confirmed, nodding his assent. Joker frowned but said nothing, instead deciding to brave Rupert's porridge. Jack admired his courage.

By now the mess was full with the Normandy's crew. Two tables down Jack could see Jacob sitting with the group of marines that had been angry with him earlier. Out of the corner of his eye he spotted Miranda sneaking back into her office with a few pieces of fruit. Shepard stood up, looking at Jack.

"Be ready to go ashore, Lieutenant." She said as she picked up her tray.

"Yes Commander."

"Also if I were you I'd leave the sniper in the armoury, grab yourself an assault rifle instead, we'll be mainly close quarters."

"Will do Commander." He said returning to his food.

Joker waited until Shepard had left before he spoke.

"Hey, Walker." He said getting Jack's attention.

"What is it Joker?" he asked. Joker looked around to make sure no one was listening before he leaned across the table.

"The stuff I said earlier…" he paused, "It was just bravado. A show of loyalty etc."

"Uh huh." Jack said understanding.

"So…are we cool? I don't want to be ambushed on my way back to the cockpit. I can't tell you how awkward it would be trying to fly this thing while my legs are in splints."

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**I know that this episode isn't really that action-packed, but I promise the next one will be! **

**So until then...**

**P.S. I will be starting another fanfic that will be written at the same time as this one. I wont spoil the surprise for you guys but what I will say is that it is not another Mass Effect fanfic, but it is a video game one! So I'm going to keep trying to update this story every Monday as promised but if for some reason it doesn't appear on Monday then it may mean there wont be one for that week and that I'll be writing for my new fic. But as I said, I'm going to try and write them alongside one another, so please be patient. :) **


	6. Chapter 6

**A/N: Sorry I didn't post last Monday, I've been busier than I expected and also I've been working on my new fanfic, which hopefully the first chapter should be ready for next week or the week after. I hope you enjoy this chapter! As always feel free to review etc. any opinion or advice is welcomed. If you want to ask a question then feel free as I'm always happy to answer them!**

**Disclaimer: I do not own the Mass Effect universe or any of its character, with the exception of Jack Walker, he is my creation.**

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Chapter 6

Ellen Shepard had never been to Omega before, something that she considered a mercy.

The brutal smells of waste and alcohol had assaulted her senses constantly since they had arrived. Walker had told her that the place hadn't changed in the slightest since he had last been here several years before. Jacob too was quick to point out that everything Shepard was witnessing wasn't at all unusual here.

To her left a Batarian man stood on a plinth and preached to a surprisingly large throng of people. Fortunately for her the mad prophet wasn't her concern. Her concern was getting to Professor Solus alive.

Aria T'Loak had been surprisingly forthcoming with her information regarding the Salarian, worryingly so. Shepard knew that whatever Aria had in store, her first concern was the professor.

Behind her Lieutenant Walker and Jacob talked amiably as they walked towards the entrance to the quarantine zone. They didn't seem at all concerned, something that worried Shepard all the more. Their relaxed attitude was almost arrogant, and in Shepard's experience it was often arrogance that got you killed, a trait that she witnessed first-hand many years ago. _No need to dig up the past_, she reasoned as the group approached a Turian guard. The guard was having an argument with a human woman but as soon as he spotted three heavily armed soldiers heading his way he quickly shifted his attention.

"Turn around, lady." He ordered Shepard. She ignored him, shifting her hand so that it rested on her sidearm, something that did not escape the guards notice. Calmly she stated her business.

"There's a Salarian named Mordin Solus in the Slums." She announced, "I've got to get in there and find him."

"The doctor? Yeah, crazy bastard opened a clinic in the district a few weeks ago. The Blue Suns weren't too happy when he moved in." chuckled the guard. "I hear Mordin's trying to deal with the plague – I wish him luck!" The guard's expression hardened. "The area is still locked down though. Our orders are to wait until either the plague or the Blue Suns kill everyone – then go in and clean up."

Behind Shepard, Walker spoke up.

"Listen." He started "You're stuck here until this quarantine is over. That could take weeks." Shepard smiled slightly as she saw that the Lieutenants words were taking effect. He continued, "What you really need is to get this problem solved right now – that's what we do." He said indicating the group. "Let us in and we'll get this district straightened out."

The guard paused for a moment while he weighed Walker's words.

"You think you can fix this?" The guard asked. Walker nodded. "Why not then? Quarantine is more to keep infected people in anyway. I'll radio ahead, tell them you're coming in." With that he moved out of the way, to be followed quickly by the human woman who appeared to be now apocalyptic in her anger. The guard rolled his eyes as he switched on his radio. Shepard turned to her team.

"When we go in I want weapons out and eyes peeled. We're walking into a warzone so stay alert." She looked between the two Cerberus men to make sure they understood before they entered.

The group moved slowly as they advanced into the quarantine zone. Their weapons were shouldered at all times, their eyes watching for any sign of conflict. Shepard led the group, followed by Walker in the middle and Jacob covering the rear. They moved from cover to cover, checking all the angles. In the distance the ringing of an alarm was ever-present, a reminder that they were never safe.

"Target's ahead." Shepard whispered behind her. At the end of the street two Blue Suns were standing lazily by the entrance to a home. One guard was resting against a wall whilst the other appeared to be checking his data pad. Nearby Shepard could see piles of corpses that had been set alight. The putrid smell of burnt flesh made her feel slightly nauseous.

"Walker, on my go you take the one on the left and I'll take the one on the right." She looked behind and Jack nodded as he crouched and took aim.

"Three. Two. One. Go!" In perfect synchronisation the two men dropped. Shepard kept her slights trained on the men in case either moved. After a few seconds she was satisfied that they weren't getting back up.

"Did you hear that?" Jacob asked scanning the area. Jack moved off to the right.

"Yeah, it came from over here." He confirmed. They approached cautiously before rounding the corner. Shepard was repulsed by what they found. Lying against a wall was a Batarian man, his clothes covered in vomit and filth. _A plague victim_, she thought sighing. The Batarian raised his head at the sound of people.

"Humans." He spat, "Should have guessed. Bad enough that you infect us with this plague, now you lack the decency to even wait until I die before you come to steal my possessions." He spluttered, a raking cough engulfing him.

Shepard knelt down in front of him. "Is there anything I can do for you?" she asked sincerely.

"Get away from me human!" He pulled a gun from behind him. Walker and Jacob raised their weapons before Shepard waved them away. The Batarian was unaware of the guns being trained on him as he continued his rant. "Your kind has done too much already. Your plague did this to me." He spat accusingly. "Your feigned pity, is the final insult."

Shepard stood, towering over the dying man.

"I need to find Mordin Solus."

"Humans looking for human sympathiser! I hope the Vorcha burn your friend Mordin and his clinic to the ground!" Again he was consumed by a cough, this time flecks of blood spattered his already stained clothes. "I hope you…I…dammit! Damn you!" The Batarian crumpled over as he was crippled by choking.

"Hey! Stay with me!" Shepard pulled up her Omni-tool.

Without hesitation she bent down and gave the sick man some medication.

"This won't cure the plague, but it might help a bit."

After a few hesitant seconds the Batarian cautiously pushed himself to his feet, using the wall as a support.

"You…you helped me. Why?"

Shepard simply smiled.

"That's what I do." She said with a shrug. "I don't know if I can find a cure for this plague but I'm damn well going to try." She promised. In front of her she noticed a change in the Batarian. Whereas before he had been tense and defensive, he appeared to relax, his body position shifted and the previous hatred in his eyes had died.

"Mordin has a clinic on the far side of the district. He's taking in refugees, offering to help those affected by the plague." He paused, debating whether to continue, "I was afraid to go to him before – he's dangerous, but perhaps he can help."

"Dangerous how?" Walker enquired. The Batarian shifted uncomfortably.

"The Blue Suns tried to press him for protection money. He killed them. He stunned them with some kind of toxin, then just gunned them down. He's not just a doctor. Doctors don't execute people and display their bodies as a warning."

Shepard was intrigued.

Before she had imagined the professor as a typically skittish Salarian whose only purpose would be to create the counter-measure and hide in the realtive safety of the Normandy.

Now though, she was curious. _Looks like the Illusive Man did his homework_. She turned back to the Batarian.

"When I find Mordin I'll tell him about you. If he has a cure then I'll make sure someone gets it to you." She promised the man.

"Thank you." Was all he said in reply, he didn't need to say anything else, words meant nothing in the face of the kindness he had been shown today.

Shepard turned to her companions with an excited grin.

"Let's go find our dangerous doctor."

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**I hope you enjoyed the chapter :) I know that it's a bit shorter than most but the conversation with the sick Batarian lasted longer than I had anticipated and I wasn't sure when another good opportunity to break would come around. Hopefully it'll be back to usual with another chapter next monday, but if not then it doesn't mean I've stopped writing, it just means it'll be uploaded another day. Also next week I hope to be announcing my new fanfic, so hooefully when I do you'll check it out! Until the next time...**


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